Strange loops: journeys in declarative logic programming in genomics and beyo...

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Describes building a Prolog-based toolkit BitKit for genomic queries, a Make-like workflow system biom that runs on clusters, and a compact query layer SPARQLProg that compiles reusable Horn-rule fragments to SPARQL; reports OWL/description-logic reasoners failing on real ontologies while a datalog-based pipeline scales to classify large OBO ontologies, describes an undecidable Common Logic alternative obog and the widely adopted LinkML schema toolchain with monthly community calls and early OntoGPT/CurateGPT assistants.

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" chapters (14)

1. 0:00Introduction and background
2. 3:31Declarative bioinformatics
3. 5:40Bitkit tool development
4. 8:06Logic to SQL compilation
5. 9:50Community reception
6. 11:26Workflow automation
7. 15:57Ontologies and description logics
8. 21:09OBOlog and common logic
9. 25:55Standardization in ontologies
10. 28:41Semantic web queries
11. 34:57LinkML introduction
12. 37:59LinkML tools and metamodel
13. 40:08LinkML Datalog
14. 43:22Future with AI and conclusion